I think it's only a Warning level. Happened to me too. I was exactly doing what you mentioned also, I guess there are more sysadmins has same common sense too.
The problem was shown in this error message:
$ /usr/local/bin/jekyll --version
WARN: Unresolved specs during Gem::Specification.reset:
jekyll-watch (~> 1.1)
WARN: Clearing out unresolved specs.
Please report a bug if this causes problems.
/usr/local/lib/ruby/gems/2.2/gems/bundler-1.14.6/lib/bundler/runtime.rb:40:in `block in setup': You have already activated liquid 3.0.6, but your Gemfile requires liquid 4.0.0. Prepending `bundle exec` to your command may solve this. (Gem::LoadError)
from /usr/local/lib/ruby/gems/2.2/gems/bundler-1.14.6/lib/bundler/runtime.rb:25:in `map'
from /usr/local/lib/ruby/gems/2.2/gems/bundler-1.14.6/lib/bundler/runtime.rb:25:in `setup'
from /usr/local/lib/ruby/gems/2.2/gems/bundler-1.14.6/lib/bundler.rb:100:in `setup'
from /usr/local/lib/ruby/gems/2.2/gems/jekyll-3.4.1/lib/jekyll/plugin_manager.rb:36:in `require_from_bundler'
from /usr/local/lib/ruby/gems/2.2/gems/jekyll-3.4.1/exe/jekyll:9:in `<top (required)>'
from /usr/local/bin/jekyll:22:in `load'
from /usr/local/bin/jekyll:22:in `<main>'
The solution is I think it would be better to not messing with
Gemfile or the locks since the
bundle update is taking a good care for it, so either I should decide to rollback liquid to version 3.0.6 or to override the jekyll command by prepending
bundle exec. I picked the last option.
It works as workaround, for example:
$ which jekyll
$ bundle exec /usr/local/bin/jekyll --version
Tue Mar 7 08:32:39 JST 2017
So far so good with my blog, so..yes it's bothering but if it still works, I'll leave it as per it is. Will debug it if somehow making more serious error.